You might want to take a look at
this question on SO. Then, one option, is to derive your own MongoRepository and (internally) handle the
Query.WithinCircle etc. using the Collection property of the MongoRepository and creating of Geospatial indices in the repository's constructor for example.

In the end it's entirely up to you; you do what you prefer and implement it as you like. MongoRepository is little more than a thin IRepository interface over the actual C# driver.